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PURPOSE To compare the 36-month outcomes of mechanical or transepithelial phototherapeutic keratectomy (PTK) epithelial removal before accelerated corneal crosslinking (CXL) for pediatric keratoconus. SETTING Atatürk Training and Research Hospital, Ankara, Turkey. DESIGN Retrospective case series. METHODS Eyes that had accelerated CXL after mechanical (Group 1) or transepithelial PTK (Group 2) epithelial removal were evaluated preoperatively and 12, 24, and 36 months postoperatively. The uncorrected (UDVA) and corrected distance visual acuities, spherical equivalent (SE), manifest astigmatism, and corneal tomographic and aberrometric parameters were assessed. RESULTS The study included 40 eyes of 35 consecutive keratoconus patients younger than 18 years with a 36-month follow-up. Group 1 comprised 15 patients, and Group 2 comprised 20 patients. Both groups had a significant improvement in UDVA (P = .001 and P = .02, respectively) and a significant decrease in maximum keratometry (K) and thinnest corneal thickness (all P < .001) 36 months postoperatively. The improvements in maximum K, topographic astigmatism, and spherical aberration were greater in Group 2 than in Group 1 at 12 months (P = .03, P = .01, and P = .04, respectively). After 12 months, the outcomes in the 2 groups were more similar. CONCLUSIONS The initial visual and topographic outcomes of transepithelial PTK ablation were better than those of mechanical epithelium removal before accelerated CXL in pediatric patients with keratoconus. Over the long-term, the results were similar between the 2 groups.